Variant simulator; report

Node used for reconstructing ancestral genome sequence

If a (newick) phylogenetic tree file has been provided, the visualisation of the MSA used in the calculations is shown below. The two chosen groups (i.e. ‘ingroup’ / species of interest, and outgroup) are highlighted in the tree. The outgroup, used in the computation or not, is the outgroup, which together with the reference species of interest coalesce at the node of interest, from which the ancestral sequence have been extracted. Most recent common ancestor (MRCA) is highlighted in purple and labeled. The rest of the clades in the alignment are shown in lighter grey. Regardless whether a reconstructed ancestral sequence at a node, or an outgroup, has been chosen as the ancestor, the MRCA will be highlighted.

Distribution of simulated variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of simulated variants is shown across the genome of the species of interest. The grey distribution corresponds to the total amount of simulated variants, whereas the red distribution corresponds to the subset that is overlapping with a corresponding non-gap ancestral sequence. If there is no forced sub-sampling due to lack of ancestral sequence, the distribution will be fully red.

Distribution of derived variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of derived variants is shown across the genome of the species of interest. The distribution of derived variants across the genome is shown in red.

How much of the reference genome that has an available, aligned reconstructed ancestral sequence

Table 1 Fraction of refence genome that has an available aligned reconstructed ancestral sequence. The leftmost column represents the total size of the source chromosome (in base pairs), from the species of interest. The middle column represents the size (in base pairs) of the recontructed ancestral genome (or size of aligned outgroup without gaps). The rightmost column represents the fraction of the reference genome that is covered by an ancestral sequence, i.e. the fraction of the reference with a corresponding non-gap ancestral alignment.
Size of ref. genome Size of reconstructed genome Fraction covered of ref. genome
1 277 851 379 66 396 801 0.24
2 145 549 147 30 578 806 0.21
3 136 770 423 27 769 000 0.20
4 130 488 646 25 506 433 0.20
5 106 564 835 21 382 231 0.20
6 165 568 887 36 200 919 0.22
7 121 779 005 27 074 055 0.22
8 138 913 488 28 493 809 0.21
9 138 776 831 29 208 182 0.21
10 73 781 108 11 630 205 0.16
11 79 373 231 14 273 688 0.18
12 61 428 131 11 726 337 0.19
13 208 716 492 45 957 035 0.22
14 141 217 515 29 015 747 0.21
15_17 203 673 900 39 117 516 0.19
16 79 833 563 18 793 500 0.24
18 55 909 202 11 921 214 0.21

Number of simulated variants

and how many are overlapping with an available ancestral sequence

Table with corresponding data:
Table 2.
Fraction of simulated SNPs that is overlapping with a reconstructed ancestral sequence. Column explanation from left to right:
i) chromosome number
ii) the total number of simulated SNPs
iii) the number of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
iv) the fraction of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
v) the total number of derived variants.
No of sim. SNPs Number of sim. SNPs overlapping ancestral seq. Fraction of sim. SNPs overlapping ancestral seq. Number of derived variants
1 22 927 644 5 280 279 0.23 4 209 724
2 11 521 337 2 351 831 0.20 1 987 404
3 11 017 857 2 140 660 0.19 1 796 664
4 9 690 582 1 798 554 0.19 1 635 245
5 8 140 487 1 525 271 0.19 1 363 294
6 14 155 433 2 959 072 0.21 2 358 690
7 10 126 906 2 132 350 0.21 1 733 737
8 10 765 518 2 120 466 0.20 1 888 182
9 11 010 436 2 220 127 0.20 1 919 192
10 5 181 040 767 340 0.15 789 214
11 5 783 835 979 858 0.17 940 246
12 4 941 773 913 334 0.18 745 254
13 15 935 441 3 329 464 0.21 2 916 604
14 10 703 794 2 123 606 0.20 1 830 163
15_17 14 615 013 2 605 186 0.18 2 472 730
16 6 884 197 1 549 499 0.23 1 240 541
18 4 706 393 953 691 0.20 783 897

Types of simulated mutations

Table with corresponding data:
Table 3
Fraction of mutation types across the simulated variants with an available corresponding ancestral sequence. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions
v) the fraction of CpG site mutations
vi) the fraction of non-CpG mutations (transitions + transversions)
No. of SNPs Fraction transitions Fraction transversions Fraction CpGs Fraction non-CpGs (1-CpGs)
1 5 280 279 0.51 0.31 0.18 0.82
2 2 351 831 0.47 0.29 0.24 0.76
3 2 140 660 0.45 0.27 0.27 0.73
4 1 798 554 0.48 0.30 0.22 0.78
5 1 525 271 0.48 0.30 0.22 0.78
6 2 959 072 0.46 0.28 0.26 0.74
7 2 132 350 0.48 0.29 0.22 0.78
8 2 120 466 0.50 0.31 0.19 0.81
9 2 220 127 0.49 0.30 0.21 0.79
10 767 340 0.45 0.27 0.28 0.72
11 979 858 0.47 0.29 0.24 0.76
12 913 334 0.40 0.24 0.36 0.64
13 3 329 464 0.52 0.32 0.17 0.83
14 2 123 606 0.47 0.28 0.25 0.75
15_17 2 605 186 0.49 0.30 0.21 0.79
16 1 549 499 0.51 0.32 0.17 0.83
18 953 691 0.47 0.29 0.24 0.76

Types of derived mutations*

  • CpG mutation information is not available.

##### Table with corresponding data:

Table 4
Fraction of mutation types across the derived variants. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions.
No. of SNPs Fraction transitions Fraction transversions
1 4 209 724 0.62 0.38
2 1 987 404 0.62 0.38
3 1 796 664 0.61 0.39
4 1 635 245 0.62 0.38
5 1 363 294 0.62 0.38
6 2 358 690 0.62 0.38
7 1 733 737 0.62 0.38
8 1 888 182 0.61 0.39
9 1 919 192 0.62 0.38
10 789 214 0.60 0.40
11 940 246 0.60 0.40
12 745 254 0.61 0.39
13 2 916 604 0.63 0.37
14 1 830 163 0.63 0.37
15_17 2 472 730 0.62 0.38
16 1 240 541 0.62 0.38
18 783 897 0.62 0.38

Visualisation of gene density

and CDS overlap

Validation of simulation parameters

Number of mutations, fractions, and substitution rates. To make sure the simulation was performed as expected, the leftmost part is the calculated numbers and rates in the parameter files, including the total number of simulated variants per chromosome, based on information from the ancestor and reference species. The middle part is the (re)calculated numbers and rates based on the total number of simulated variants. The rightmost part is the (re)calculated numbers and rates within the subset with a corresponding non-gap ancestral sequence. The comparison of parameters and simulated variants is to make sure that the simulation has been perform as intended, and the comparison between total set and the subset is to make sure that the distribution is the same even if the variants are forced to be down-sampled due to the lack of an available ancestral sequence.

Comparison of numebr of mutations between log files and actual simulated files
Parameter files
Simulated variant file
Simulated variant file
(filtered for positions with a corresponding non-gap ancestral position)
Chromosome considered: 1 Chromosome considered: 1 Chromosome considered: 1
Total mut: 4827345 Total mut: 18161574 Total mut: 4356214
#AC AG AT #AC AG AT #AC AG AT
336961 823109 272737 1374900 3167269 977064 334445 768760 236989
6.98% 17.05% 5.65% 7.57% 17.44% 5.38% 7.68% 17.65% 5.44%
#CA CG CT #CA CG CT #CA CG CT
157024 138714 685399 551178 546249 2459393 130048 129229 579072
3.25% 2.87% 14.20% 3.03% 3.01% 13.54% 2.99% 2.97% 13.29%
#GA GC GT #GA GC GT #GA GC GT
687517 139186 158171 2459521 547243 550892 580295 128684 130379
14.24% 2.88% 3.28% 13.54% 3.01% 3.03% 13.32% 2.95% 2.99%
#TA TC TG #TA TC TG #TA TC TG
272024 820044 336459 977767 3169874 1380224 236775 767214 334324
5.64% 16.99% 6.97% 5.38% 17.45% 7.60% 5.44% 17.61% 7.67%
Total CpG mut: 651630 Total CpG mut: 4766070 Total CpG mut: 924065
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
56926 46325 221615 403599 369709 1609977 78036 71493 312889
8.74% 7.11% 34.01% 8.47% 7.76% 33.78% 8.44% 7.74% 33.86%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
222914 46453 57397 1607169 371185 404431 311614 71744 78289
34.21% 7.13% 8.81% 33.72% 7.79% 8.49% 33.72% 7.76% 8.47%
Chromosome considered: 2 Chromosome considered: 2 Chromosome considered: 2
Total mut: 2264703 Total mut: 26630670 Total mut: 6142157
#AC AG AT #AC AG AT #AC AG AT
172849 391957 121834 1995289 4598634 1417532 466741 1072736 330938
7.63% 17.31% 5.38% 7.49% 17.27% 5.32% 7.60% 17.47% 5.39%
#CA CG CT #CA CG CT #CA CG CT
67919 71674 306816 819329 813096 3659674 186264 184876 829324
3.00% 3.16% 13.55% 3.08% 3.05% 13.74% 3.03% 3.01% 13.50%
#GA GC GT #GA GC GT #GA GC GT
307000 71695 68131 3660767 813093 820234 830963 184189 186805
13.56% 3.17% 3.01% 13.75% 3.05% 3.08% 13.53% 3.00% 3.04%
#TA TC TG #TA TC TG #TA TC TG
121206 392022 171600 1419629 4606632 2006761 330242 1071853 467226
5.35% 17.31% 7.58% 5.33% 17.30% 7.54% 5.38% 17.45% 7.61%
Total CpG mut: 320795 Total CpG mut: 7818311 Total CpG mut: 1489953
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
26772 25867 107943 662261 606066 2641207 126029 115021 504133
8.35% 8.06% 33.65% 8.47% 7.75% 33.78% 8.46% 7.72% 33.84%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
107521 25750 26942 2637623 608184 662970 502579 115915 126276
33.52% 8.03% 8.40% 33.74% 7.78% 8.48% 33.73% 7.78% 8.48%
Chromosome considered: 3 Chromosome considered: 3 Chromosome considered: 3
Total mut: 2052400 Total mut: 34266539 Total mut: 7701058
#AC AG AT #AC AG AT #AC AG AT
168948 368461 104584 2543696 5857281 1805926 579801 1332448 411463
8.23% 17.95% 5.10% 7.42% 17.09% 5.27% 7.53% 17.30% 5.34%
#CA CG CT #CA CG CT #CA CG CT
56438 65259 262990 1070423 1063170 4781137 236657 235291 1054661
2.75% 3.18% 12.81% 3.12% 3.10% 13.95% 3.07% 3.06% 13.70%
#GA GC GT #GA GC GT #GA GC GT
264065 65064 56963 4781834 1062484 1071251 1056558 234225 237507
12.87% 3.17% 2.78% 13.95% 3.10% 3.13% 13.72% 3.04% 3.08%
#TA TC TG #TA TC TG #TA TC TG
104671 365319 169638 1806785 5867451 2555101 409885 1331931 580631
5.10% 17.80% 8.27% 5.27% 17.12% 7.46% 5.32% 17.30% 7.54%
Total CpG mut: 300781 Total CpG mut: 11200299 Total CpG mut: 2071712
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
24263 25558 99974 948345 868418 3783234 175451 159933 700747
8.07% 8.50% 33.24% 8.47% 7.75% 33.78% 8.47% 7.72% 33.82%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
100483 26010 24493 3779731 871421 949150 699119 161002 175460
33.41% 8.65% 8.14% 33.75% 7.78% 8.47% 33.75% 7.77% 8.47%
Chromosome considered: 4 Chromosome considered: 4 Chromosome considered: 4
Total mut: 1900296 Total mut: 41376212 Total mut: 9097577
#AC AG AT #AC AG AT #AC AG AT
152898 345115 102206 3074963 7078581 2182783 685787 1576406 486664
8.05% 18.16% 5.38% 7.43% 17.11% 5.28% 7.54% 17.33% 5.35%
#CA CG CT #CA CG CT #CA CG CT
53170 54824 240738 1290274 1282445 5764949 278638 277295 1242089
2.80% 2.89% 12.67% 3.12% 3.10% 13.93% 3.06% 3.05% 13.65%
#GA GC GT #GA GC GT #GA GC GT
243846 55082 53733 5767200 1280428 1292833 1245202 276377 279514
12.83% 2.90% 2.83% 13.94% 3.09% 3.12% 13.69% 3.04% 3.07%
#TA TC TG #TA TC TG #TA TC TG
101595 344469 152620 2183059 7091058 3087639 485575 1576927 687103
5.35% 18.13% 8.03% 5.28% 17.14% 7.46% 5.34% 17.33% 7.55%
Total CpG mut: 227830 Total CpG mut: 13781208 Total CpG mut: 2473747
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
19307 17946 76216 1167112 1068509 4655535 209401 191262 836769
8.47% 7.88% 33.45% 8.47% 7.75% 33.78% 8.46% 7.73% 33.83%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
76585 18148 19628 4651037 1071379 1167636 834929 191978 209408
33.61% 7.97% 8.62% 33.75% 7.77% 8.47% 33.75% 7.76% 8.47%
Chromosome considered: 5 Chromosome considered: 5 Chromosome considered: 5
Total mut: 1576641 Total mut: 47261847 Total mut: 10287021
#AC AG AT #AC AG AT #AC AG AT
124704 285074 84276 3509800 8079096 2491251 776234 1784172 550738
7.91% 18.08% 5.35% 7.43% 17.09% 5.27% 7.55% 17.34% 5.35%
#CA CG CT #CA CG CT #CA CG CT
44144 45895 203142 1475571 1466617 6594791 314288 312608 1402299
2.80% 2.91% 12.88% 3.12% 3.10% 13.95% 3.06% 3.04% 13.63%
#GA GC GT #GA GC GT #GA GC GT
203602 45895 44709 6596594 1464360 1478123 1405908 312034 315005
12.91% 2.91% 2.84% 13.96% 3.10% 3.13% 13.67% 3.03% 3.06%
#TA TC TG #TA TC TG #TA TC TG
84386 284743 126071 2490651 8092040 3522953 549620 1786192 777923
5.35% 18.06% 8.00% 5.27% 17.12% 7.45% 5.34% 17.36% 7.56%
Total CpG mut: 187087 Total CpG mut: 16036060 Total CpG mut: 2809574
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
15958 14737 62768 1358374 1243473 5416399 238036 217434 949980
8.53% 7.88% 33.55% 8.47% 7.75% 33.78% 8.47% 7.74% 33.81%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
62997 14660 15967 5412560 1246498 1358756 948149 218037 237938
33.67% 7.84% 8.53% 33.75% 7.77% 8.47% 33.75% 7.76% 8.47%
Chromosome considered: 6 Chromosome considered: 6 Chromosome considered: 6
Total mut: 2688313 Total mut: 57265499 Total mut: 12485602
#AC AG AT #AC AG AT #AC AG AT
217796 480362 135525 4223711 9717827 2997768 935304 2150255 664121
8.10% 17.87% 5.04% 7.38% 16.97% 5.23% 7.49% 17.22% 5.32%
#CA CG CT #CA CG CT #CA CG CT
74509 86462 350433 1806537 1796158 8077797 386094 383105 1722204
2.77% 3.22% 13.04% 3.15% 3.14% 14.11% 3.09% 3.07% 13.79%
#GA GC GT #GA GC GT #GA GC GT
348382 86981 74906 8075943 1794170 1809861 1724169 383403 386255
12.96% 3.24% 2.79% 14.10% 3.13% 3.16% 13.81% 3.07% 3.09%
#TA TC TG #TA TC TG #TA TC TG
135551 479200 218206 2995800 9731787 4238140 661769 2151807 937116
5.04% 17.83% 8.12% 5.23% 16.99% 7.40% 5.30% 17.23% 7.51%
Total CpG mut: 399550 Total CpG mut: 20187841 Total CpG mut: 3570065
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
31808 33710 133701 1710496 1565846 6817979 302645 276529 1206694
7.96% 8.44% 33.46% 8.47% 7.76% 33.77% 8.48% 7.75% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
134642 33974 31715 6813798 1568209 1711513 1204803 277207 302187
33.70% 8.50% 7.94% 33.75% 7.77% 8.48% 33.75% 7.76% 8.46%
Chromosome considered: 7 Chromosome considered: 7 Chromosome considered: 7
Total mut: 1984316 Total mut: 64674701 Total mut: 14141656
#AC AG AT #AC AG AT #AC AG AT
155552 350750 104361 4765515 10961968 3381186 1058435 2432219 750943
7.84% 17.68% 5.26% 7.37% 16.95% 5.23% 7.48% 17.20% 5.31%
#CA CG CT #CA CG CT #CA CG CT
56658 60096 264615 2045417 2032823 9141866 437965 434891 1955077
2.86% 3.03% 13.34% 3.16% 3.14% 14.14% 3.10% 3.08% 13.82%
#GA GC GT #GA GC GT #GA GC GT
265875 60123 57033 9140284 2030881 2049003 1957240 435704 438600
13.40% 3.03% 2.87% 14.13% 3.14% 3.17% 13.84% 3.08% 3.10%
#TA TC TG #TA TC TG #TA TC TG
104182 349157 155914 3377036 10970964 4777758 748554 2432615 1059413
5.25% 17.60% 7.86% 5.22% 16.96% 7.39% 5.29% 17.20% 7.49%
Total CpG mut: 276990 Total CpG mut: 22905545 Total CpG mut: 4046361
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
22409 21714 93520 1941049 1776592 7735436 342961 313416 1367754
8.09% 7.84% 33.76% 8.47% 7.76% 33.77% 8.48% 7.75% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
94646 21923 22778 7731423 1779306 1941739 1365421 314290 342519
34.17% 7.91% 8.22% 33.75% 7.77% 8.48% 33.74% 7.77% 8.46%
Chromosome considered: 8 Chromosome considered: 8 Chromosome considered: 8
Total mut: 2214898 Total mut: 72995081 Total mut: 15855647
#AC AG AT #AC AG AT #AC AG AT
176470 402473 126225 5405834 12436606 3834957 1192870 2742130 846682
7.97% 18.17% 5.70% 7.41% 17.04% 5.25% 7.52% 17.29% 5.34%
#CA CG CT #CA CG CT #CA CG CT
64407 61317 278042 2291092 2276967 10243012 486714 483343 2173800
2.91% 2.77% 12.55% 3.14% 3.12% 14.03% 3.07% 3.05% 13.71%
#GA GC GT #GA GC GT #GA GC GT
277883 61345 64404 10239692 2274859 2295856 2176408 484481 487718
12.55% 2.77% 2.91% 14.03% 3.12% 3.15% 13.73% 3.06% 3.08%
#TA TC TG #TA TC TG #TA TC TG
125286 401225 175821 3830915 12445779 5419512 844505 2742605 1194391
5.66% 18.11% 7.94% 5.25% 17.05% 7.42% 5.33% 17.30% 7.53%
Total CpG mut: 239410 Total CpG mut: 25350683 Total CpG mut: 4452836
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
21258 18444 79781 2148911 1965904 8560602 377549 344814 1504844
8.88% 7.70% 33.32% 8.48% 7.75% 33.77% 8.48% 7.74% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
79828 18809 21290 8556487 1969533 2149246 1503159 345759 376711
33.34% 7.86% 8.89% 33.75% 7.77% 8.48% 33.76% 7.76% 8.46%
Chromosome considered: 9 Chromosome considered: 9 Chromosome considered: 9
Total mut: 2224676 Total mut: 81335718 Total mut: 17618784
#AC AG AT #AC AG AT #AC AG AT
173928 395884 121464 6030722 13874609 4279326 1326234 3048469 941119
7.82% 17.80% 5.46% 7.41% 17.06% 5.26% 7.53% 17.30% 5.34%
#CA CG CT #CA CG CT #CA CG CT
64868 66309 291354 2547747 2532543 11388497 540469 536929 2412508
2.92% 2.98% 13.10% 3.13% 3.11% 14.00% 3.07% 3.05% 13.69%
#GA GC GT #GA GC GT #GA GC GT
293039 66384 65278 11389103 2530686 2552896 2416844 538057 541198
13.17% 2.98% 2.93% 14.00% 3.11% 3.14% 13.72% 3.05% 3.07%
#TA TC TG #TA TC TG #TA TC TG
119986 392881 173301 4275369 13887877 6046343 938700 3050443 1327814
5.39% 17.66% 7.79% 5.26% 17.07% 7.43% 5.33% 17.31% 7.54%
Total CpG mut: 276406 Total CpG mut: 28020482 Total CpG mut: 4909826
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
23472 21783 93054 2374668 2173401 9462689 416139 380214 1659620
8.49% 7.88% 33.67% 8.47% 7.76% 33.77% 8.48% 7.74% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
93346 21390 23361 9457230 2176499 2375995 1656921 381383 415549
33.77% 7.74% 8.45% 33.75% 7.77% 8.48% 33.75% 7.77% 8.46%
Chromosome considered: 10 Chromosome considered: 10 Chromosome considered: 10
Total mut: 935415 Total mut: 84821208 Total mut: 18171027
#AC AG AT #AC AG AT #AC AG AT
89612 179152 48185 6287594 14466953 4462285 1367669 3144714 970781
9.58% 19.15% 5.15% 7.41% 17.06% 5.26% 7.53% 17.31% 5.34%
#CA CG CT #CA CG CT #CA CG CT
22144 27757 102040 2657109 2641711 11879725 557279 553581 2487351
2.37% 2.97% 10.91% 3.13% 3.11% 14.01% 3.07% 3.05% 13.69%
#GA GC GT #GA GC GT #GA GC GT
101308 27551 22245 11878847 2639853 2663461 2491358 554743 557884
10.83% 2.95% 2.38% 14.00% 3.11% 3.14% 13.71% 3.05% 3.07%
#TA TC TG #TA TC TG #TA TC TG
47956 178000 89465 4457797 14481152 6304721 968710 3146932 1370025
5.13% 19.03% 9.56% 5.26% 17.07% 7.43% 5.33% 17.32% 7.54%
Total CpG mut: 102503 Total CpG mut: 29716032 Total CpG mut: 5124923
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
8217 9083 33967 2518767 2304333 10035659 434497 396906 1732216
8.02% 8.86% 33.14% 8.48% 7.75% 33.77% 8.48% 7.74% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
33765 9261 8210 10029630 2308108 2519535 1729443 397978 433883
32.94% 9.03% 8.01% 33.75% 7.77% 8.48% 33.75% 7.77% 8.47%
Chromosome considered: 11 Chromosome considered: 11 Chromosome considered: 11
Total mut: 1106347 Total mut: 88954709 Total mut: 18918893
#AC AG AT #AC AG AT #AC AG AT
94718 206212 61089 6601521 15189495 4684587 1426353 3278620 1012204
8.56% 18.64% 5.52% 7.42% 17.08% 5.27% 7.54% 17.33% 5.35%
#CA CG CT #CA CG CT #CA CG CT
30279 31320 129108 2781666 2765191 12435550 578598 575174 2583730
2.74% 2.83% 11.67% 3.13% 3.11% 13.98% 3.06% 3.04% 13.66%
#GA GC GT #GA GC GT #GA GC GT
128926 31382 30088 12436088 2763694 2787706 2587860 576258 579431
11.65% 2.84% 2.72% 13.98% 3.11% 3.13% 13.68% 3.05% 3.06%
#TA TC TG #TA TC TG #TA TC TG
61556 206693 94976 4681752 15207200 6620259 1010502 3281731 1428432
5.56% 18.68% 8.58% 5.26% 17.10% 7.44% 5.34% 17.35% 7.55%
Total CpG mut: 117162 Total CpG mut: 31366366 Total CpG mut: 5356915
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
10338 9503 38565 2658637 2432129 10592831 454077 414765 1810653
8.82% 8.11% 32.92% 8.48% 7.75% 33.77% 8.48% 7.74% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
38936 9504 10316 10586724 2436686 2659359 1808018 415920 453482
33.23% 8.11% 8.80% 33.75% 7.77% 8.48% 33.75% 7.76% 8.47%
Chromosome considered: 12 Chromosome considered: 12 Chromosome considered: 12
Total mut: 835976 Total mut: 92021016 Total mut: 19505650
#AC AG AT #AC AG AT #AC AG AT
75390 157665 38259 6808832 15669136 4832948 1465995 3369889 1040426
9.02% 18.86% 4.58% 7.40% 17.03% 5.25% 7.52% 17.28% 5.33%
#CA CG CT #CA CG CT #CA CG CT
19297 29361 99144 2889471 2871733 12915722 599282 595447 2675598
2.31% 3.51% 11.86% 3.14% 3.12% 14.04% 3.07% 3.05% 13.72%
#GA GC GT #GA GC GT #GA GC GT
99235 29652 19678 12919704 2870512 2895579 2680905 596816 600253
11.87% 3.55% 2.35% 14.04% 3.12% 3.15% 13.74% 3.06% 3.08%
#TA TC TG #TA TC TG #TA TC TG
37691 155496 75108 4830560 15687578 6829241 1039016 3373452 1468571
4.51% 18.60% 8.98% 5.25% 17.05% 7.42% 5.33% 17.29% 7.53%
Total CpG mut: 136256 Total CpG mut: 33241832 Total CpG mut: 5683492
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
10225 13258 44563 2817361 2577867 11226412 481587 440111 1921238
7.50% 9.73% 32.71% 8.48% 7.75% 33.77% 8.47% 7.74% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
44415 13487 10308 11219818 2582795 2817579 1918328 441162 481066
32.60% 9.90% 7.57% 33.75% 7.77% 8.48% 33.75% 7.76% 8.46%
Chromosome considered: 13 Chromosome considered: 13 Chromosome considered: 13
Total mut: 3325413 Total mut: 104558105 Total mut: 22280498
#AC AG AT #AC AG AT #AC AG AT
212563 546978 192910 7762253 17860833 5509467 1679717 3861045 1191923
6.39% 16.45% 5.80% 7.42% 17.08% 5.27% 7.54% 17.33% 5.35%
#CA CG CT #CA CG CT #CA CG CT
117607 94401 498706 3265942 3246543 14598692 680943 676971 3040327
3.54% 2.84% 15.00% 3.12% 3.11% 13.96% 3.06% 3.04% 13.65%
#GA GC GT #GA GC GT #GA GC GT
499534 94439 118596 14605937 3245915 3274193 3046398 678492 682535
15.02% 2.84% 3.57% 13.97% 3.10% 3.13% 13.67% 3.05% 3.06%
#TA TC TG #TA TC TG #TA TC TG
192724 544129 212826 5509569 17890818 7787943 1190946 3867897 1683304
5.80% 16.36% 6.40% 5.27% 17.11% 7.45% 5.35% 17.36% 7.56%
Total CpG mut: 459183 Total CpG mut: 36640184 Total CpG mut: 6238108
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
41116 30469 157049 3105381 2841403 12373764 528546 483044 2108856
8.95% 6.64% 34.20% 8.48% 7.75% 33.77% 8.47% 7.74% 33.81%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
158774 30601 41174 12366589 2847115 3105932 2105139 484357 528166
34.58% 6.66% 8.97% 33.75% 7.77% 8.48% 33.75% 7.76% 8.47%
Chromosome considered: 14 Chromosome considered: 14 Chromosome considered: 14
Total mut: 2065412 Total mut: 112290930 Total mut: 23873569
#AC AG AT #AC AG AT #AC AG AT
155078 358534 108153 8322273 19149736 5905728 1795382 4128001 1273450
7.51% 17.36% 5.24% 7.41% 17.05% 5.26% 7.52% 17.29% 5.33%
#CA CG CT #CA CG CT #CA CG CT
61573 63254 285959 3515620 3495848 15715792 731951 727880 3269252
2.98% 3.06% 13.85% 3.13% 3.11% 14.00% 3.07% 3.05% 13.69%
#GA GC GT #GA GC GT #GA GC GT
288769 63110 61842 15724749 3493938 3525497 3275350 729376 734002
13.98% 3.06% 2.99% 14.00% 3.11% 3.14% 13.72% 3.06% 3.07%
#TA TC TG #TA TC TG #TA TC TG
107874 356619 154647 5906889 19185001 8349859 1273251 4136163 1799511
5.22% 17.27% 7.49% 5.26% 17.09% 7.44% 5.33% 17.33% 7.54%
Total CpG mut: 329802 Total CpG mut: 39611153 Total CpG mut: 6768643
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
26311 24860 113561 3357804 3072739 13375455 573827 524244 2287618
7.98% 7.54% 34.43% 8.48% 7.76% 33.77% 8.48% 7.75% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
113183 24838 27049 13369035 3078620 3357500 2283820 525821 573313
34.32% 7.53% 8.20% 33.75% 7.77% 8.48% 33.74% 7.77% 8.47%
Chromosome considered: 15_17 Chromosome considered: 15_17 Chromosome considered: 15_17
Total mut: 2836203 Total mut: 122931515 Total mut: 25931846
#AC AG AT #AC AG AT #AC AG AT
199185 489498 162723 9117778 20981955 6470538 1954389 4494664 1386379
7.02% 17.26% 5.74% 7.42% 17.07% 5.26% 7.54% 17.33% 5.35%
#CA CG CT #CA CG CT #CA CG CT
93263 79232 394570 3843989 3824007 17186003 792246 788085 3538790
3.29% 2.79% 13.91% 3.13% 3.11% 13.98% 3.06% 3.04% 13.65%
#GA GC GT #GA GC GT #GA GC GT
393513 79192 92231 17198247 3821575 3855477 3545415 789380 794626
13.87% 2.79% 3.25% 13.99% 3.11% 3.14% 13.67% 3.04% 3.06%
#TA TC TG #TA TC TG #TA TC TG
162247 491146 199403 6470531 21014200 9147215 1385779 4502645 1959448
5.72% 17.32% 7.03% 5.26% 17.09% 7.44% 5.34% 17.36% 7.56%
Total CpG mut: 369705 Total CpG mut: 43585581 Total CpG mut: 7315552
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
33159 26989 124681 3694656 3381563 14717161 620165 566587 2472318
8.97% 7.30% 33.72% 8.48% 7.76% 33.77% 8.48% 7.74% 33.80%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
124773 27109 32994 14709675 3388195 3694331 2468021 568719 619742
33.75% 7.33% 8.92% 33.75% 7.77% 8.48% 33.74% 7.77% 8.47%
Chromosome considered: 16 Chromosome considered: 16 Chromosome considered: 16
Total mut: 1439760 Total mut: 128339522 Total mut: 27210587
#AC AG AT #AC AG AT #AC AG AT
106022 246001 80504 9531498 21929015 6763086 2053397 4721170 1456456
7.36% 17.09% 5.59% 7.43% 17.09% 5.27% 7.55% 17.35% 5.35%
#CA CG CT #CA CG CT #CA CG CT
45624 41992 196771 4007557 3987161 17918398 830274 825752 3708557
3.17% 2.92% 13.67% 3.12% 3.11% 13.96% 3.05% 3.03% 13.63%
#GA GC GT #GA GC GT #GA GC GT
195871 41493 45131 17928154 3983250 4018884 3714922 826759 832652
13.60% 2.88% 3.13% 13.97% 3.10% 3.13% 13.65% 3.04% 3.06%
#TA TC TG #TA TC TG #TA TC TG
81252 252552 106547 6761630 21954355 9556534 1455612 4727375 2057661
5.64% 17.54% 7.40% 5.27% 17.11% 7.45% 5.35% 17.37% 7.56%
Total CpG mut: 180278 Total CpG mut: 45061771 Total CpG mut: 7586310
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
16120 13196 61241 3819983 3496258 15215268 643287 587706 2563369
8.94% 7.32% 33.97% 8.48% 7.76% 33.77% 8.48% 7.75% 33.79%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
60850 13338 15533 15208202 3502521 3819539 2559535 589777 642636
33.75% 7.40% 8.62% 33.75% 7.77% 8.48% 33.74% 7.77% 8.47%
Chromosome considered: 18 Chromosome considered: 18 Chromosome considered: 18
Total mut: 913485 Total mut: 131737572 Total mut: 27939471
#AC AG AT #AC AG AT #AC AG AT
79887 172695 45205 9780769 22502083 6940386 2108408 4846285 1495250
8.75% 18.91% 4.95% 7.42% 17.08% 5.27% 7.55% 17.35% 5.35%
#CA CG CT #CA CG CT #CA CG CT
22546 27205 108222 4115628 4095135 18404208 852785 848176 3809783
2.47% 2.98% 11.85% 3.12% 3.11% 13.97% 3.05% 3.04% 13.64%
#GA GC GT #GA GC GT #GA GC GT
107882 27263 22197 18412263 4090674 4127433 3815695 849088 855357
11.81% 2.98% 2.43% 13.98% 3.11% 3.13% 13.66% 3.04% 3.06%
#TA TC TG #TA TC TG #TA TC TG
45242 174808 80333 6937715 22525933 9805345 1494173 4852431 2112040
4.95% 19.14% 8.79% 5.27% 17.10% 7.44% 5.35% 17.37% 7.56%
Total CpG mut: 107689 Total CpG mut: 46370114 Total CpG mut: 7811117
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
8532 9426 35945 3930962 3597633 15657559 662337 605062 2639427
7.92% 8.75% 33.38% 8.48% 7.76% 33.77% 8.48% 7.75% 33.79%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
35946 9248 8592 15649841 3603996 3930123 2635388 607236 661667
33.38% 8.59% 7.98% 33.75% 7.77% 8.48% 33.74% 7.77% 8.47%